MEXICO CITY—Mexican authorities have issued an arrest warrant on charges of racketeering and the use of illegally obtained funds for Javier Duarte, the governor of Mexico’s third-largest state, a top federal government official said Wednesday.

An official from Mexico’s Attorney General’s office said the whereabouts was unknown of Mr. Duarte, who last week took a leave of absence as governor of the oil-rich state of Veracruz to face the accusations. He was last heard from on Oct. 13, according to Flavino Rios, the acting governor...